Hi Matthias, if a tool prints something to the stderr that is indeed considered to indicate a failure, and it's the default mostly because we don't want to break legacy tools that make this assumption. If you include a profile version in your tool or change your command section to <command detect_errors="exit_code"></commands> this will more reasonably determine if a tool failed based on the exit code. To me this sounds like something that really should be fixed in the tool as presumably this affects every deployer. Best, Marius On Mon, 27 Aug 2018 at 11:52, Matthias Bernt <m.bernt@ufz.de> wrote:
Dear list,
I'm struggling to set java options for galaxy tools. Currently I use `<env file="job_setup_script.sh"/> in my job_conf.xml and in the script I explored two ways to set java options:
`_JAVA_OPTIONS="-Xmx5G -Xms1G -Djava.io.tmpdir=/work/songalax/tmp"`
But then java prints "Picked up _JAVA_OPTIONS: ..." to stderr which is be interpreted as error by some tools. If I'm correct this is currently the default .. I have seen this happening, but can't remember the name of the tool.
So I switched to this 'trick':
`alias java='java -Xmx5G -Xms1G -Djava.io.tmpdir=/work/songalax/tmp'`
but the problem is that the tool script is called and not sourced and therefore aliases are not used (could this be changed?). Furthermore, for tools which explicitly set the java options my settings would be ignored anyway (an example is the MSGFPlusAdapter which calles `java -Xmx3500m` .. so my -Xmx is overwritten .. I passing GALAXY_MEMORY_MB to the corresponding parameter might be a solution for this tool).
Any thought or suggestions on how to set the parameters in a production environment are very welcome.
Cheers, Matthias
--
------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann ------------------------------------------- ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/